science communication

Biosphere definition: “The biosphere is the global sum of all ecosystems. It can also be termed as the zone of life on Earth, a closed system (apart from solar and cosmic radiator and heat from the interior of the Earth), and largely self-regulating”

The Earth is Biosphere I. At Christmas time, I visited the infamous Biosphere II. Located near the town of Oracle in Arizona, Biosphere II now owned by the University of Arizona, is a glass and steel structure covering 3.15 acres (1.28 hectares) of what was once Sonoran desert. Financed by Texas oil billionaire, Ed Bass and inspired by Synergerian John Allen who has been described as either a visionary or a cult leader, Biosphere II was built in 1987 and designed to house five different Earth environments or biomes–fog desert, savannah, tropical rainforest, mangrove swamp, and ocean–along with a small farm, in a closed system, without oxygen or water exchange with the outside world. It was to be a large scale experiment to see what life might be like for future Martian colonists living in similar bubbles, along with its less publicized mission to find out if biospheres could function as refuges (Refugia) for small groups of people to survive nuclear war or other disasters.

Generating a great deal of excitement around the world, on Sept. 26, 1991, eight Biospherians, four men and four women, entered Biosphere II and sealed themselves in for a planned two year experiment to see if they could live in a sustainable self-contained system, growing all of their own food and recycling all of their wastes and water. Almost from the outset, the grand experiment was plagued with many problems including: the Biospherians couldn’t grow enough food to sustain themselves; many of the 3,800 Biosphere species, from hummingbirds to bees perished, disrupting the poorly designed ecosystems’ balances; and the bacteria in the soil and compost overproduced carbon dioxide and depleted the oxygen, forcing the Biosphere managers to pump oxygen into the structure to keep the crew alive.

One of the most interesting and unexpected problems of the mission came from the Biospherians themselves. Confined in an isolated environment, starving, and suffering the effects of low oxygen levels, the crew separated into two bitter factions, first arguing over the purpose of the experiment and later about almost everything. So bad was the split between the two groups that it inspired the Dutch developers of a new TV series which we now know as Big Brother.

On Sept. 26, 1993, the grand experiment ended as the crew emerged out of the Biosphere II’s airlock into Biosphere I. At the time and even now, many view the Biosphere II experiment as a failure. In 1999, Time Magazine included Biosphere II in its list of 100 worst ideas. But nearly 150 scientific papers have been published on the results from the experiment, ranging from to structural engineering to invasive ant species dominance to physiological changes due to caloric deprivation to the effects of drought on tropical rainforests. It has been acknowledged that much of what is known about ocean acidification was originally discovered in studies done in Biosphere II. Biosphere II has also contributed to our better understanding of the carbon cycle and oxygen dynamics, soil nutrients and agricultural productivity, and bioremediation and waste water reclamation. And despite ongoing problems and changing ownership, Biosphere II is still being used for scientific research. Now part of the University of Arizona it is involved in many projects, including the landscape evolution observatory, rainforest drought manipulations. No longer a closed system, visitors are allowed inside on guided tours through the biomes and the south lung. Here are a few photos from my visit:

The two sections I found most interesting were the ocean biome and the south lung. When you enter the ocean biome, you hear a massive, regular boom like a heart beat; it’s the sound of the vacuum wave generator and makes the Biosphere seem like a living thing. It’s oddly comforting. The ocean is made up of 3.8 million liters of seawater originally trucked in from Gulf of California and was originally designed to mimic the Caribbean Sea, complete with a coral reef and fish. When the ocean acidified during the course of the original experiment with the Biospherians, the coral reef died but there is still life in the miniature ocean. I could see bright yellow tangs swim by the underwater window; the fish are not fed by staff but are self sufficient. Out of the 47 species introduced into the ocean at the start, 11 survived the years of neglect and the yellow tang are especially successful. The reasons for their singular success are being studied. At the same time, the University of Arizona is slowly changing the ocean to become a microcosm of the Gulf of California instead of the Caribbean for future research purposes.

The south lung or variable volume pressure relief system is another fascinating stop on the Biosphere II tour and, once again, it makes the structure seem alive. There are two lungs, both large expansion chambers whose flexible membranes can move up and down to keep the pressure differential between the Biosphere II and outside atmosphere at zero and limiting the leakage rate to less than 10% –a notable achievement. Most people focus on the biomes of Biosphere II without realizing the engineering infrastructure, the Technosphere, keeping it functional.

If you ever get the chance to visit Biosphere II, it’s definitely worth it! It has been called a successful failure for not accomplishing its original goals but instead for highlighting unforeseen problems, both in terms of design and choosing personnel for future space colonies and in predicting the consequences of climate change in Biosphere I.

Biosphere has a much more colourful history than I have covered in this write up. If you are interested in learning more, here are some more links:

I came across a recent news release on Synbiota and while following links on the subject, fell down the rabbithole of biohacking. And by biohacking, I don’t mean the Quantified Self movement where people wear FitBits and other wearables to monitor and modify their physical and mental states (see my earlier blog on the QS Movement here) but instead, the brave new world of DIY-Bio where people create genetically modified organisms in the comfort of their own garages or open labs. But let’s start at the beginning. I mentioned Synbiota. This is a Canadian company which has just released a kit that allows people (citizen-scientists) to introduce red, blue, or green luminescent protein genes into a plasmid, transform the plasmid into E. coli, and enjoy the experience of seeing coloured colonies fluoresce on a plate in the dark for only $395 USD.

Cladistics. Phylogeny.Taxonomy. Doesn’t sound very interesting, does it? Well, click on this website and suddenly these subjects become much more exciting! This newly released website, the brainchild of a large group of evolutionary biologists, bioinformaticians, mathematicians, and computer scientists, was described in PNAS on September 18th of this year, followed immediately by the launch of the website. Visually stunning, it instantly caught the attention of the news mediaand science bloggers.

Funded by the US National Science Foundation, the idea behind this website is to show the evolutionary relationships between all forms of life on Earth in the form of a Tree of Life (ToL). The creators have been working collaboratively on this project since 2012, collecting hundreds of published phylogenies and synthesizing the data into one supertree. The result is what project head, Dr. Karen Cranston from Duke University, reports is “Version 1.0 (of the Tree of Life)”. By making the ToL project open source, the group hopes that other researchers will upload and share their phylogenetic data and modify any incorrect data while students, educators, and the public will treat the website as “a Wikipedia for evolutionary trees”.

An entry from the Open Tree of Life

Image Owned by eTreeoflife.com (CC0 Public Domain)

Cranston called the open ToL a “draft” or Version 1.0 ToL for several reasons. First, during the preliminary collection of over 7,000 published trees, the open ToL creators quickly realized that most of the data was available only as journal figures rather than in electronic form. Only 500 trees were digitally accessible and these were what was used to construct the ToL, leaving out the data from the other 6,500 trees. Second, there are many gaps in the ToL. For example, the open ToL creators note that there are large gaps in Kingdoms Bacteria, Fungi, Nematoda, and Insecta between the estimated number of species and what is present in published trees. The current ToL only includes 1 out of about 10 estimated insect species and 1 out of 100 nematode species. Even more important, the ToL only shows 1 out of an estimated 10 million bacterial species! Third, some of the branchings in the ToL are still being debated. There is an ongoing argument between the hypothesis that eukaryotes are embedded within Archaea and the belief that Eukaryae and Archaea are separate. And four, the definition of a species can be blurred by mechanisms such as horizontal gene transfer where genes from one species, for example, bacterial carotenoid biosynthesis genes, can be transferred to and incorporated into another species, the pea aphid in this case. This gene transfer means there is an unexpected link or branch between two unrelated species from different kingdoms. As Alastair Crisp of the University of Cambridge observes, “the degree of horizontal gene transfer we’re finding means the tree of life looks a bit like a strangling fig”. (By the way, did you know humans have about 150 foreign genes in their genome? But, that’s another blog post….)

While Douglas Soltis from the University of Florida, one of the creators of open ToL, admits their ToL is Version 1.0, he stills marvels that “twenty-five years ago, people said this goal of supertrees was impossible. The open ToL is an important starting point that other investigators can now refine and improve for decades to come”. Will you be one of those researchers who adds a species or branch to the open ToL or develops more software for this model? You could be!

On January 19, 2006, when I was in Grade 2 and playing with Transformers, the New Horizons spacecraft blasted off on its mission to explore Pluto (New Horizons, 2015). Nine years later, I’m in Grade 11, and 4.4 billion kilometers away, the spacecraft arrived at its destination in July.

Last Thursday (Sep 17, 2015), NASA released photos of Pluto taken by New Horizons spacecraft July 14, 2015, 15 minutes after its closest approach. One of the most arresting images is this backlit photo of Pluto which highlights Pluto’s atmosphere.

Pluto’s atmosphere was the source of much speculation before the flyby of New Horizons provided data. Because the dwarf planet is so far away from the Sun (an average of 39.5 astronomical units or more than 40 times farther from the Sun than Earth) and so small (2,370km in diameter or slightly smaller than our Moon), it had been difficult to determine if Pluto had an atmosphere and if so, what its characteristics were (Talbert, 2015; Wild, 2015). By studying occultation data from June 9, 1988, (Millis et al 1993) provided the most conclusive data up to that point that Pluto appeared to have an atmosphere and in the same year, the presence of methane, nitrogen, and carbon monoxide were confirmed (Owen et al, 1993). These images of Pluto’s atmosphere confirm its presence and data collected from the early approach of New Horizon’s to Pluto support the atmospheric composition (Singer & Stern, 2015).

Pluto’s average surface temperature is about -2300C (McGovern, 2006) and this has implications for the dwarf planet’s atmosphere. Before the images from New Horizons, it was thought that the atmosphere might be hazy as a result of the solid methane and other ices sublimating off the surface (Clancy, 2002). The images from New Horizons have definitively confirmed the speculated haze (SSERVI, 2015).

Pluto’s atmosphere brings up one other intriguing question. With the dwarf planet being so small, having an atmospheric pressure only 1/1000th that of earth’s (Lellouche, 2009) and its distant, elliptical orbit which is currently moving it farther away from the minimal heat of the Sun, it has been speculated that Pluto’s atmosphere may “freeze out” and collapse (Stern & Trafton, 1984; Elliot et al, 2007). However, recent observations suggest that this may not happen (Olkin et al, 2015). Further information from New Horizons may provide an answer. We’ll just have to wait! I’ve waited nine years, I can wait a little longer.

“You are in a boat directly over the Mariana Trench. If you drop a 7kg bowling ball over the side, how long would it take to hit the bottom?” How would you answer this silly question? Well, if you’re Randall Munroe, you give it some serious thought, do some research and calculations, and then answer the question scientifically. (Answer: 2 hours 20 minutes.) I recently discovered “Xkcd. what if” (http://what-if.xkcd.com) –a weekly blog where, since 2012, Randall Munroe gives (mostly) serious scientific answers to ridiculous hypothetical questions posted to his site by readers. Although Munroe is currently a cartoonist, he was a NASA roboticist and has a background in physics and mathematics so he is familiar with scientific method. Munroe’s approach to answering ridiculous questions, for example, “what in my pocket actually contains more energy, my Zippo or my smartphone? What would be the best way of getting the energy from one to the other? And since I am already feeling like Bilbo in this one, is there anything else in my pocket that would have unexpected amounts of stored energy?” is similar to that of the Mythbusters, answering the original question (the Zippo lighter has more energy than the smartphone and there have been some attempts to power smartphones with fuel cells), and then taking it to another, more absurd, level (the other item in your pocket that would have more energy, about 500 watt-hours, if burned, is your hand or a sandwich).

One of Munroe’s illustrations

Image Owned by Randall Munroe (CC0 Public Domain)

Many of the silly questions lead to interesting and sometimes unexpected answers. For example, in answer to the question “what is the farthest from Earth that any Earth thing has died?,” Munroe points out that a 2008 paper estimated that individual spacecraft carried about 1.98 x 1011 microorganisms, even after being “sterilized.” (There’s a real job position at NASA for spacecraft sterilization and, as Munroe enthusiastically informs the reader, it comes with the best job title ever–Planetary Protection Officer!) Using that number, he then calculates that several thousand Earth microorganisms may still be alive, and some of them dying, on the Voyageur 1 space probe which is currently 1.9 x 1010 kilometers distant from Earth .

The cartoonist recently published a compilation of some of his blog posts in book form. It’s titled “What If: Serious Scientific Answers to Absurd Hypothetical Questions” and is really enjoyable and informative to read, especially the sections where he includes some of the weird and worrying, questions he doesn’t answer. Here are a couple of examples—“what is the total nutritional value (calories, fat, vitamins, minerals, etc) of the average human body?” and “what temperature would a chainsaw need to be at to instantly cauterize any injuries inflicted with it?.”

So, if you have a silly, but not weird and disturbing, question that has been keeping you awake at night, just go to the website and submit your question. It might be answered!

Last Christmas, my (maternal) grandparents received an unusual present—they had their genomes sequenced! Well, not their entire genomes (because that would cost about $1,000 USD) but part of their genomes. For 1/10th the cost, they each had about 602,000 of their 10 million SNPs sequenced. SNPs or Single Nucleotide Polymorphisms are places in a person’s genome where one of the nucleotides (A, G, C or T) can be substituted for another; a source of genetic variation that occurs in more than 1% of the population. (This site has a good SNPs figure.) SNPs occur about once every 300 nucleotides and can be in the DNA sequences between genes, acting as biological markers for nearby disease related genes, or within genes where they can directly affect gene expression. Most SNPs do not affect health but some do, affecting responses to certain drugs, susceptibility to toxins and other environmental factors, and the risk of developing certain diseases.

Before presenting the results of the genetic risk factors and inherited conditions, the company carefully stated that the results should be discussed with your doctor and to realize that this doesn’t necessarily mean you will or will not develop a specific condition since there are other genetic variants linked to these conditions that weren’t tested for. The company also pointed out that environmental and lifestyle factors can contribute to these diseases. Before being able to see the results, Opa and Gramma had to read a legal document and click that they understood. Only then, could they see the results. However, Opa and Gramma are lucky, they’re Canadian so they actually have access to the health analyses; people in the US do not. Americans can only see the results of the ancestry analyses at the moment because the FDA (Food and Drug Administration) has classified 23andMe’s DNA sequencing test as an unapproved medical device).

My Grandmother’s Ancestry

Among the inherited conditions where the company reported whether the variant was present or absent included sickle cell anemia, cystic fibrosis, phenylketonuria and Tay-Sachs Disease while among the genetic risk factors, variants were reported as present or absent for celiac disease, Alzheimer’s disease, Parkinson’s Disease and breast cancer (BRCA1 and 2) along with others. Since Opa and Gramma both know what diseases run in their families, the results from these two analyses didn’t come as any surprise. However, the drug response analyses were unexpected and potentially life-saving. It turns out one of my grandparents has a predicted increased sensitivity to one family of drugs and the other has a higher than normal risk of myopathy if they take statins. These are useful pieces of information that they can tell their doctors if medications need to be prescribed.

Another analysis done on my grandparents’ DNA was ancestry composition. Here’s a screen grab of my grandmother’s ancestral analysis: The analysis showed what percentage of her DNA came from each of the world’s 31 populations. In her case, she is 99.3% European, 0.4% East Asian and native American, 0.1% Middle Eastern and North African, 0.1% subSaharan and 0.1% unassigned. She also has 2.5% Neanderthal DNA! [The average is between 1-4%.] This information isn’t very useful but it is interesting and shows how interconnected the human race is.

So, did my grandparents find having (some of) their genome sequenced worth it? Yes. Did it provide some useful information? Yes. Will I be getting mine done at some point? Definitely!

On January 17, 2013, journalist Ann Finkbeiner wrote a blog “What I am not going to do” in which she said that she would be writing an article on a prominent astronomer’s research without referring the astronomer’s gender, spouse, childcare arrangements or how the researcher was taken aback by the competitiveness of the field or nutured students. Finkbeiner objected to the common practice of focusing on the fact that a researcher is a woman rather than on her work. After reading Finkbein’s blog post, fellow journalist Christie Aschwanden reposted it on her own blog and proposed the Finkbeiner Test. To pass the test, she said an article on a female scientist must not mention the following facts:
1. The fact that she’s a woman
2. Her husband’s job
3. Her child care arrangements
4. How she nurtures her underlings
5. How she was taken aback by the competitiveness in her field
6. How she’s such a role model for other women
7. How she’s the “first woman to…”
What is another way to tell if an article is gender biased? Aschwanden suggested reading a post about a female scientist and then mentally switching the gender to male. If the descriptions or observations made about the female scientist sounded ridiculous when said about a man, then those comments should not be in the article.

The assignment this week was to write a reverse Finkbeiner. In other words, write an article about a male scientist that would fail every one of the seven rules of the Finkbeiner test. I decided to write a reverse Finkbeiner obituary for Albert Einstein in response to the obituary written in the New York Times for rocket scientist Yvonne Brill.

On April 18, 1955, Dr. Albert Einstein (known affectionately as “Albertl “ by his wife) passed away as a result of an abdominal aortic aneurysm, after refusing treatment. He leaves behind five children; father to Lieserl, Hans Albert, and Eduard (called “Tete” by his loving father) by his first wife and stepfather to Ilse and Margot by his second wife. Mileva Maric, his first wife, was a successful physicist who, to Albert’s life long sorrow, divorced him after he made some poor personal decisions. Albert’s second wife, Elsa, was also his cousin, meaning that his children Ilse and Margot were also his first cousins once removed.

Today was the second full session during which we could work on our original projects. We all began working on our projects, promptly at 4:30. During the past two weeks, we had all been working hard to complete our research and to collect all the materials we would require for the construction of our projects. There were still a fairly large number of people who wished to continue researching during this session, which meant that about 50% of us were starting to build our project, whilst the other 50% were on our computers looking up information. We had laid out our timelines within our proposals, so after a little while working on our projects, we were asked to write our goals for the session on the board and to check off the ones that were complete.

The Voynich Manuscript is a hand written document, of which 240 pages remain, written on calf skin vellum, illustrated with diagrams, drawings, and an unknown language written from left to right. It was purchased in Italy in 1912 by Polish book dealer Wifrid Voynich who owned it until his death in New York in 1930. Later donated to Yale University, it is now in the Beinecke Rare Book and Manuscript Library.

You know how when you have been searching online for information on a specific subject, the ads that pop up for the next while are all on that subject? Well, I had recently been doing some research on 3D printers and a few days ago while looking for something unrelated online, one of those pop up ads caught my eye. It said “3D printed vaccines.” 3D printed vaccines!?! Intrigued, I followed the link and discovered a whole new area of 3D printing research.

Since about 2009, geneticist and entrepreneur Dr. Craig Venter and his team have been working on digesting biological molecules and medicines into data that can be compiled in a computer file that can be read by a 3D printer (The video can be found here). So far, they have developed an early version which is currently being tested.